title: Control_2

city: nanjing

first: qiang

last: tian

address: School of Life Sciences, Nanjing University, Nanjing, 210023, China.

department: the school of life sciences

institute: nanjing university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Subcutaneous adipose tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Subcutaneous adipose tissue

value: ADSC

value: mesenchymal stem cell

value: primary adipocyte differentiation


title: NJT2_3

status: Public on May 21 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment

value: primary adipocyte differentiation with NJT-2


title: NJT2_1


title: Sample4, replicate 2, scRNAseq [D_CMO_1_S11]

city: Santa Cruz

first: Camilla

last: Forsberg

state: California

address: 1156 High Street

country: USA

institute: Institute for the Biology of Stem Cells, University of California Santa Cruz

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data was initially processed via the 10X Genomics Cell Ranger Cloud pipeline, using the mouse genome (mm10) modified to allow for detection of reporter transgene RNA expression. For the downstream analysis, cells with expression of fewer than 200 genes were excluded, and genes detected in fewer than three cells were removed from subsequent analysis steps. Mitochondrial and ribosomal gene transcripts, as well as Malat1 transcripts, were removed to reduce technical bias. This resulted in a dataset of 22,790 cells and 22,870 genes. Additionally, 13 cells with absent Kit RNA were filtered out. Doublets identified by DoubletDetection 2.4.0 (p_thresh=1e-16, voter_thresh=0.5) removed 157 cells in total (Gayoso et al. 2018).  The UMI counts for each cell were normalized by the total counts across all genes (target_sum=1e4), and log-transformed with an added pseudo count of 1.
Assembly: mm10
Supplementary files format and content: comma-separated values files and matrix files

source_name: Bone Marrow

extract_protocol:
Cells were harvested and c-Kit-enriched from the long bones and hips of the hind legs of young and old mice as described above. Cc-Kit-enriched cells were then stained for lineage markers via a purified rat-anti-mouse antibody cocktail (CD3, CD4, CD5, CD8, CD11b, B220, Gr-1, and Ter119) on ice for 30 minutes. Cells were washed three times followed by incubation with goat-anti-rat Alexa Fluor 680 secondary on ice in the dark for 20 minutes. Cells were washed three times then resuspended in blocking solution (10% bovine calf serum (BCS), 10% normal mouse serum (Invitrogen), and 10% normal rat serum (Invitrogen) in 1X PBS (Cytiva). Cells were blocked for 10 minutes on ice in the dark. Following block, directly conjugated antibodies were directly added to the cells (CD117/cKit and CD150) and incubated on ice in the dark for 45 minutes, gently mixing the cells at the 30-minute mark. A small aliquot of cells was also used to perform a CD150 fluorescence minus one (FMO) control. Cells were washed three times, resuspended in 10% BCS in 1X PBS (wash buffer), with three drops of propidium iodide (diluted 1:5000 in wash buffer) added. Live, lineage-c-Kit+CD150- and live, lineage-c-Kit+CD150+ young and old cells were sorted on a BD FACSAria IIu (BD Biosciences) (Figure S6). The CD150- and CD150+ gates were touching to ensure a continuum of cells across CD150 expression were sorted. Cells were sorted into chilled 1X PBS (without Mg2+) containing 20% BCS and checked for sort purity. Following sorting, cells were washed and each of the four sorted populations (young CD150-, young CD150+, old CD150-, and old CD150+) were split into three aliquots for Cell Multiplexing Oligo (CMO) labeling (10X Genomics) following manufacturer’s instructions, with each individual group of cells receiving a single unique CMO tag. Cells were washed three times with wash buffer and manually counted via a hemocytometer. When possible, equal numbers of cells from each of the 12 CMO labeled aliquots were combined to artificially inflate the numbers of rare CD150+ cells and to equalize numbers between young and old mice. The pooled cells were then split into two replicates for further processing.
Both pooled replicates were used in parallel in the Chromium Next GEM single Cell 3’ v3.1 protocol (10X Genomics) following manufacturer’s directions. GEM generation and barcoding was performed immediately post-sorting, with resulting samples stored at -20ºC per manufacturer’s instructions. All other steps were performed simultaneously for all samples from each of the two independent experiments. Following library construction, samples were assessed via an Agilent Bioanalyzer with a High Sensitivity chip (Agilent Technologies). Final sample libraries were sequenced on a Novaseq P100 at the University of California Davis DNA Technologies and Expression Analysis Core, targeting 50,000 read pairs per cell for the gene expression libraries and 5,000 reads per cell for the CMO libraries.

value: Bone Marrow

value: HSPC

value: C57Bl/6, FlkSwitch


title: NJT2_2


title: Sample3, replicate 2, scRNAseq [C_CMO_1_S10]

description: 10x Genomics


title: Control_1


title: Sample2, replicate 2, scRNAseq [B_CMO_1_S9]

description: 10x Genomics


title: Sample1, replicate 2, scRNAseq [A_CMO_1_S8]

description: 10x Genomics


title: RNA-seq: Infected BSCL2het 10

city: Natal

first: Selma

middle: MB

last: Jeronimo

state: Rio Grande do Norte

address: 655 Av Passeio dos Girassois, Capim Macio

department: Tropical Medicine Institute (IMT-RN)

country: Brazil

institute: Federal University of Rio Grande do Norte (UFRN)

description:
1.INF.lane1
1.INF.lane2
1.INF.lane3

data_processing:
Illumina HiSeq 2000 (75 bp, paired-end), each sample with 3 experimental replicates (with the exception of participant 6, who has only an experimental duplicate in the infected sample.)
Aligmntent HISAT2 2.2.0 in default parameters
Files were compressed into BAM using Samtools 1.15
The counts assigned were accessed by FeatureCounts
Differential expression analysis: DESeq2 3.14 (Bioconductor)
Assembly: GRCh38
Supplementary files format and content: Gene counts matrix from FeatureCounts of all samples together

organism: Homo sapiens

source_name: monocytes-derived macrophages

growth_protocol: PBMC were maintained in RPMI 1640 supplemented with 1.5μM L-glutamine, 1mM Hepes, 10% heat-inactivated AB human serum and 5ng/mL of M-CSF (Gibco, USA) to obtain monocytes-derived macrophages.

extract_protocol:
RNA extraction was performed using the standard Trizol protocol, followed by purification in the Qiagen column. The quality of the RNA was checked using the NanoDrop spectrometer (NanoDrop Technologies), Agilent Bioanalyzer (RNA Nano Chip, Agilent) and also by Qubit 2.0 / 3.0 fluorometer.
20 ul of total RNA (75-350 ng/ul) were submitted to the sequencing facility and default protocol was carried on.

treatment_protocol: Infection with L. infantum (Strain isolated from a patient diagnosed with VL in Natal, RN, Brazil) proceeded in the monocyte-derived macrophages. Leishmania stationary promastigotes at a 5 parasites/cell ratio were incubated for 2 hours. After the incubation, free parasites were washed with warm RPMI 1640. Infected MØ for sequencing were aliquoted at 72 hours after infection.

value: monocytes-derived macrophages

tag: Sex

value: male

value: BSCL2 heterozygous

value: Infected (Leishmania infantum)


title: Sample2, replicate 2, scRNAseq [B_GEL_1_S1]

description: 10x Genomics


title: Sample3, replicate 2, scRNAseq [C_GEL_1_S2]

description: 10x Genomics


title: RNA-seq: Infected BSCL2het 8

description:
12.INF.lane1
12.INF.lane2
12.INF.lane3

value: female


title: Sample4, replicate 2, scRNAseq [D_GEL_1_S3]

description: 10x Genomics


title: Sample1, replicate 2, scRNAseq [A_GEL_1_S12]

description: 10x Genomics


title: Sample4, replicate 1, scRNAseq [D_CMO_1_S12]

description: 10x Genomics


title: Sample4, replicate 1, scRNAseq [D_GEL_1_S4]

description: 10x Genomics


title: Sample1, replicate 1, scRNAseq [A_GEL_1_S1]

description: 10x Genomics


title: Sample3, replicate 1, scRNAseq [C_GEL_1_S3]

description: 10x Genomics


title: Steady state wild type bone marrow CD55+ myeloid progenitors Proteome_targeted

city: Liege

first: Christophe

middle: J

last: Desmet

address: B34, Avenue de l'Hopital 1

country: Belgium

institute: University of Liege

description:
CD11b/Sca-1/F4-80/CD117/CD150/Fcer1a/CCR3/CD29/CD170/CD55
Totalseq-B CITE-seq

library_source: other

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Data analysis was performed using Seurat V4 (v4.3.0)  in R (v4.0.3)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files as output from CellRanger
Supplementary files format and content: rds file as Seurat output
Library strategy: CITE-seq

molecule: other

extract_protocol:
Fixed myeloid progenitors (CD45+ CD55+ CD115- Ly6g- CD90.2- NK1.1- CD45R-) were sorted using a BD FACSAria III (BD Biosciences) cell sorter and were submitted to probe hybridization using the Chromium Fixed RNA Kit, Mouse Transcriptome (10X Genomics, 1000495). In total, 16,000 hybridized cells were submitted to the 10X Genomics Flex pipeline for encapsulation aiming for a recovery of 10,000 sequenced single cells as described in the manufacturer’s instructions (Chromium Next GEM Chip Q Single Cell Kit 10X Genomics, 1000422) .
Sequencing libraries were prepared using Fixed RNA Feature Barcode Kit (10X Genomics, 1000419) following the CG00047  user guide from 10X Genomics and cDNA quality and quantity were controlled using Agilent High Sensitivity DNA Kit (Agilent) on a 2100 Bioanalyser (Agilent).
scRNA-Seq and CITE-seq with Totalseq B antibodies

tag: strain

value: CD55+ Myeloid progenitors

value: wild type

tag: library type

value: GDO


title: Sample1, replicate 1, scRNAseq [A_CMO_1_S9]

description: 10x Genomics


title: Sample2, replicate 1, scRNAseq [B_GEL_1_S2]

description: 10x Genomics


title: Control_3

value: Subcutaneous adipose tissue


title: Steady state wild type bone marrow CD55+ myeloid progenitors Transcriptome

description:
Chromium Fixed RNA Kit, Mouse Transcriptome probe set
10x Genomics Flex technology

value: mRNA


title: wild type IL33 D7 SiglecF positive bone marrow leukocytes

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Data analysis was performed using Seurat V4 (v4.3.0)  in R (v4.0.3)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
SiglecF positive bone marrow leukocytes were sorted using a BD FACSAria III (BD Biosciences) cell sorter and were resuspended in Ca and Mg free PBS containing 0.4mg/ml of UltraPure™ BSA (Thermofisher, AM2616).In total, 16,000 sorted cells were submitted to the 10X Genomics pipeline for encapsulation aiming for a recovery of 10,000 sequenced single cells as described in the manufacturer’s instructions.
Sequencing libraries were prepared using Chromium Single Cell 3' Reagent Kit V3 (10X Genomics) as per manufacturer’s instructions and cDNA quality and quantity were controlled using Agilent High Sensitivity DNA Kit (Agilent) on a 2100 Bioanalyser (Agilent).

value: SiglecF positive bone marrow leukocytes

value: daily intraperitoneal injections of 400ng IL-33 in 200µl PBS  for 7 days


title: Stage_IV_IL33_Anti-IL5_Eosinophilia_1

data_processing:
Sequenced reads were aligned and mapped to the mouse genome (mm10) with RNA-Seq Alignment (Version:2.0.2) using STAR_2.6.1a on BaseSpace (https://basespace.illumina.com).
Normalization and analysis of the obtained data was performed using DESeq2 R package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Assembly: mm10
Supplementary files format and content: Tab-delimited file describing the number of reads mapped to each gene as obtained with RNA-Seq Alignment (Version:2.0.2) on BaseSpace (https://basespace.illumina.com).

extract_protocol:
For every mL of TRIzol, 200uL of chloroform was added, and the samples were vigorously mixed and incubated for 2 minutes at room temperature. Samples were centrifuged at 10,000xg for 15 minutes at 4°C to separate the phases. The RNA-containing upper aqueous phase was transferred to a new microcentrifuge tube containing 475uL of isopropanol and 2uL of glycoblue (ThermoFisher, AM9515). Samples were centrifuged at 10,000xg for 15 minutes and supernatant was discarded. One volume of 75% ethanol was added and samples were centrifuged at 10,000xg for 1 minute to precipitate the RNA and discard the supernatant. RNA pellet was resuspended in 40uL of DNase/RNase-free water for a 15-minute DNase treatment (Zymo Research, E1010). DNase treatment was followed by column-based RNA purification with the RNA Clean & concentrator-5 kit (Zymo Research, R1016). Briefly, 100uL of RNA binding buffer was added to every 50L sample and mixed thoroughly. One volume of 100% ethanol was added and the sample was transferred into a Zymo-Spin IC column in a collection tube. Columns were centrifuged at 10,000xg for 30 seconds and flow-through was discarded. The column was washed once with RNA prep buffer and twice with RNA wash buffer, following the manufacturer’s instructions. RNA was eluted in 10uL of DNase/RNase-free water. Purified RNA integrity and quantity was assessed using the RNA 6000 Pico kit (Agilent) for the presence of 18s and 28s rRNA peaks.
Full length cDNA was prepared from isolated RNA using SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio, 634889) following the manufacturer's instructions, with 17 cycles of cDNA amplification. Final cDNA quality was assessed using Agilent High Sensitivity DNA kit (Agilent, 5067-4626). cDNA libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina, FC-131-1024) using the manufacturer’s instructions.

treatment_protocol: Single cell suspensions of murine bone marrow from CB57BL/6 donor mice that received daily intraperitoneal injections of 400 ng recombinant murine IL-33 for 7 days combined with 3 daily intraperitoneal injections of 400 µg of Anti-IL5 or control isotype starting with the last IL-33 injection were first stained for Ly6G-FITC (BioLegend, 127606), CD90.2-FITC (BioLegend, 140204), NK1.1-FITC (eBioscience, 11-5941-85), CD45R-FITC (eBioscience, 11-0452-85) for 30 minutes on ice. Samples were immunomagnetically enriched for cells of interest using EasySep™ FITC positive selection kit II (Stemcell, 17682) as described by the manufacturer’s instructions. The negative fractions were subsequently stained for CD29-pacblue (BioLegend, 102224), F4/80-BV510 (BioLegend, 123125), Siglec-F-BV711(BD Biosciences,740764), CD55-biotin-streptavidin-BV786(R&D, BAF5376, BD Biosciences, 563858), CD117-BB700 (BD Biosciences, 566414), Pir-A/B-PE (BioLegend, 144104) and CD200R3-PE-cy7 (BioLegend, 142212) in 1X BD Horizon™ Brilliant stain buffer (BD Biosciences, 563794) for 30 minutes on ice. Cell suspensions were washed twice and resuspended in PBS supplemented with 5nM BD Via-Probe™ Green (BD Biosciences, 565802). cells in each of the four stages of eosinophil maturation were sorted directly into TRIzol (ThermoFisher, 15596026) using a BD FACSAria III (BD Biosciences) cell sorter with a 100μm nozzle. Sort purity was at 95 per cent or higher and samples were stored at -80°C for downstream RNA applications.

value: Bone marrow eosinophil developmental stages

value: IL33 and Anti-IL5


title: Stage_IV_IL33_Anti-IL5_Eosinophilia_3

value: Bone Marrow


title: Stage_III_IL33_Anti-IL5_Eosinophilia_3


title: Stage_IV_IL33_Anti-IL5_Eosinophilia_2


title: Stage_III_IL33_Anti-IL5_Eosinophilia_2


title: Stage_II_IL33_Anti-IL5_Eosinophilia_2


title: RNA-seq: Infected WT LV-rec 17

description:
15.INF.lane1
15.INF.lane2
15.INF.lane3

value: WT


title: Stage_II_IL33_Anti-IL5_Eosinophilia_1


title: Sample3, replicate 1, scRNAseq [C_CMO_1_S11]

description: 10x Genomics

value: HSPC

value: C57Bl/6, FlkSwitch


title: Stage_I_IL33_Anti-IL5_Eosinophilia_3


title: Stage_I_IL33_Anti-IL5_Eosinophilia_2


title: Stage_I_IL33_Anti-IL5_Eosinophilia_1


title: Sample2, replicate 1, scRNAseq [B_CMO_1_S10]

description: 10x Genomics


title: Stage_III_IL33_Ctrl_isotype_2

value: IL33 and ctrl isotype


title: Stage_III_IL33_Ctrl_isotype_1


title: Stage_IV_IL33_Ctrl_isotype_3


title: Stage_IV_IL33_Ctrl_isotype_1


title: Stage_IV_IL33_Ctrl_isotype_2


title: Stage_III_IL33_Ctrl_isotype_3


title: Stage_I_IL33_Ctrl_isotype_1


title: Stage_II_IL33_Ctrl_isotype_2


title: Stage_I_IL33_Ctrl_isotype_2


title: Cortex-505-KO8

city: Buenos Aires

first: Lucia

middle: Florencia

last: Franchini

state: Ciudad Autonoma de Buenos Aires

address: Vuelta de Obligado 2490

country: Argentina

institute: INGEBI-CONICET

data_processing:
Rhisat2. Soneson C (2023). _Rhisat2: R Wrapper for HISAT2 Aligner_. doi:10.18129/B9.bioc.Rhisat2 <https://doi.org/10.18129/B9.bioc.Rhisat2>, R package version 1.16.0, <https://bioconductor.org/packages/Rhisat2>
Rsubread::featureCounts, Rsubread version 2.14.2. Liao Y, Smyth GK and Shi W (2019). The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Research 47(8), e47.
Assembly: mm39
Supplementary files format and content: Tab delimited text file  includes raw counts of sequencing reads for mm39 genes in each sample (matrix table).

source_name: P8 Cerebral cortex

extract_protocol: RNaeasy Mini Kit (Qiagen)

value: P8 Cerebral cortex

value: 2xHAR.505 Knockout


title: Cortex-505-KO6


title: Cortex-505-KO5


title: Stage_III_IL33_Anti-IL5_Eosinophilia_1


title: Cortex-505-KO3


title: Cortex-505-KO1


title: Cortex-505-WT6

value: Wildtype


title: Cortex-505-WT5


title: 4T1 spheroids, transduced with shCtrl, replicate 3

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

country: Germany

institute: Charité University Medicine

data_processing:
Assembly: GRCm38
Sequencing reads were mapped to the GRCm38 genome using STAR aligner (v2.7.5) at default settings.
Reads mapping to genes were counted using STAR (v2.7.5).
Differentially expressed genes were determined using DESeq2 (v1.32.0).
Gene set enrichment analysis was performed using the gseKEGG function of the clusterProfiler package (v4.0.0). As input, genes were ranked according to their log fold changes shrunken with the ashr method of the DESeq2 package (v1.32.0)
Supplementary files format and content: tab-delimited file contains raw read counts for every sample.

source_name: spheroid generated from cell line

growth_protocol: Spheroids were formed with the hanging drop method and maintained in DMEM with 10% FBS at 37ºC and 5% CO2.

extract_protocol:
RNA was extracted using the Total RNA kit (Norgen) following manufacturer's instructions.
500ng of total RNA was used as input for the TruSeq RNA Library Prep Kit (Illumina) following manufacturer's instructions.

treatment_protocol: 4T1 cells were transduced with a lentivirus encoding either a control (scrambled) shRNA or Tlr7-targeting shRNA.

value: spheroid generated from cell line

value: breast cancer cells

value: shCtrl

value: expressinon of scrambled shRNA


title: Midbrain-321-KO6

source_name: E14.5 Midbrain

extract_protocol: Direct-zol RNA Miniprep Kit (Zymo Research)

value: E14.5 Midbrain

value: 2xHAR.321 Knockout


title: Cortex-505-WT4


title: Cortex-505-WT2


title: Midbrain-321-KO5


title: Midbrain-321-KO3


title: Stage_I_IL33_Ctrl_isotype_3

value: wild type


title: Stage_II_IL33_Ctrl_isotype_1

value: Bone marrow eosinophil developmental stages


title: Midbrain-321-WT6


title: Midbrain-321-KO2


title: Midbrain-321-WT5


title: TNF-a-stimulated 3

type: RNA

city: Xi'an

first: Chao

last: Fan

address: #169, Changle Road, Xincheng District

institute: The Fourth Military Medical University

description: Gene expression after 24hr with TNF-a incubation

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software v11.0.0.1 (Agilent) using Agilent GeneSpring GX v12.1 for dada standardization and to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary hepatocyte, TNF-a, 24hr, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The primay hepatocytes were cultured in hepatocyte plating/mantenance medium (Zenbio, Research Triangle, Raleigh-Durham, NC, US.)

extract_protocol: the total RNA were extracted by TRIzol reagent (CWbio, China), using the standard protocol for trizol extract. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The hepatocytes of 10E6 each well were incubated with 1μg BSA (MOCK), 1μg CD100 or 200ng TNF-a (as positive control) for stimulation.

value: primary hepatocyte

tag: donor sex

value: male

tag: donor age

tag: donor race

value: caucasian


title: Midbrain-321-WT4


title: TNF-a-stimulated 2

source_name: primary hepatocyte, TNF-a, 24hr, replicate 2


title: CD100-stimulated 3

description: Gene expression after 24hr with CD100 incubation

source_name: primary hepatocyte, CD100, 24hr, replicate 3


title: Midbrain-321-WT1


title: TNF-a-stimulated 1

source_name: primary hepatocyte, TNF-a, 24hr, replicate 1


title: Cortex-505-WT7


title: WM4237-1, mouse 1337, untreated, sample S3

city: Farmington

first: Jeffrey

middle: H

last: Chuang

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

description: Flash frozen spatial transcriptome sequencing

data_processing:
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina)
FASTQ files were split into mouse and human counterparts with Xenome 1.0.1
Mouse sequencing reads were aligned to mm10-2020-A genome with Space Ranger count 1.3.1
Human sequencing reads were aligned to GRCh38-2020-A genome with Space Ranger count 1.3.1
Human and mouse gene count matrices were merged into one matrix
Assembly: GRCh38 (GENCODE v32/Ensembl 98) and mm10 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: WM4237-1 melanoma PDX

growth_protocol: Subcutaneously implanted solid tumor on NSG mouse, passage 0

extract_protocol:
OCT-embedded fresh frozen tissue was used. Five 10µm sections from each block were used for total RNA extraction (Qiagen), which was used for RNA integrity determination by RINe score using an Agilent Tapestation and High Sensitivity RNA ScreenTape. Blocks with RINe greater than 7 were optimized for ideal permeabilization time following the vendor protocol (10x Genomics, CG000238). Sections from four tissue blocks were placed on Visium Gene Expression slide for H&E staining and brightfield imaging via NanoZoomer SQ (Hamamatsu), block-specific tissue permeabilization, mRNA capture, and subsequent library generation per the manufacturer’s protocol (10x Genomics, CG000239).
Library concentration was quantified using a Tapestation High Sensitivity DNA ScreenTape (Agilent) and fluorometry (Thermofisher Qubit) and verified via KAPA qPCR. Libraries were pooled for sequencing on an Illumina NovaSeq 6000 using a 28-10-10-90 read configuration, targeting 100,000 read pairs per spot covered by tissue.

treatment_protocol: No treatment

value: WM4237-1 melanoma PDX

tag: model


title: WM4237-1, mouse 1337, untreated, sample S4


title: L2A4: Spinal cord

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
The raw sequence reads were aligned to the rat reference genome (Rnor_6.0) using HISAT2 (version 2.0.4).
Read counting was performed with HTSeq (version 0.6.0) so that UMI duplicates were removed.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The txt file contains UMI count matrix.

organism: Rattus norvegicus

source_name: Spinal cord

extract_protocol:
Spinal cords were removed, flash frozen in liquid nitrogen, and RNA was harvested.
Library were constructed in accordance with the CEL-Seq2 protocol and prepared on the Illumina HiSeq1500 platform.

value: Sprague Dawley

value: Lower spinal cord

tag: group

value: 4 days-post injury


title: CD100-stimulated 2

source_name: primary hepatocyte, CD100, 24hr, replicate 2


title: LSK_Y604F_2

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

data_processing:
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread align function
read counts per million (CPM) were summarized at the gene level using FeatureCounts
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include counts per million (cpm) values for each Sample

growth_protocol: Mice were maintained as homozygous for Mpl mutations

extract_protocol:
RNA was harvested using Rneasy plus micro kit (Qiagen). 50 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Stranded mRNA Kit (Illumina) following manufacturer's protocols.

treatment_protocol: Bone marrow was harvested from 4 to 12 adult mice per replicate, stained with antibodies and sorted for Lin- Sca1+ Kit+ cells on a flow cytometer

value: Bone Marrow

value: Lin- Sca+ Kit+ Cells


title: LSK_Y604F_1


title: WM4237-1, mouse 1337, untreated, sample S1


title: L2A2: Spinal cord


title: WM4237-1, mouse 1337, untreated, sample S2


title: Midbrain-321-KO4


title: L2A3: Spinal cord


title: LSK_Y599F_1


title: LSK_Y599F_2


title: L2A1: Spinal cord


title: LSK_Y565F_1


title: LSK_Y565F_2


title: L2C4: Spinal cord

value: without spinal cord injury


title: Midbrain-321-WT2

value: Wildtype


title: LSK_wt_2


title: MOCK2

description: Gene expression after 24hr with BSA incubation

source_name: primary hepatocyte, BSA, 24hr, replicate 2


title: LSK_wt_1


title: L2C3: Spinal cord


title: P42_cIHC-67

city: Beijing

first: Zhiyong

last: Liu

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing:
Reads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.2.1) with default parameters.
Transcript Per Million (TPM) were calculated by StringTie  (v2.2.1) with default parameters.
Raw counts were calculated by featureCounts (v2.0.1) software.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for smartseq.

source_name: converted IHCs (cIHCs) from the cochlear outer hair cells after Tbx2 overexpression

extract_protocol:
N/A
Smart-Seq HT kit (Cat# 634437, Takara) was used to generate full-length cDNA. The cDNAs (1 ng each) were tagmented using a TruePrep DNA Library Prep Kit V2 for Illumina (Cat# TD503-02, Vazyme) and a TruePrep Index Kit V2 for Illumina (Cat# TD202, Vazyme).
Single cell full length cDNA RNA-Seq

treatment_protocol: Cochlear samples were incubated in choline chloride solution containing 20 U/mL papain (Cat# LK003178, Worthington) and 100 U/mL DNase I (Cat# LK003172, Worthington) for 20 min at 37°C, and this was followed by digestion with a protease (Cat# P5147, Sigma; 1 mg/mL) and dispase (Cat# LS02104, Worthington; 1 mg/mL) for 20 min at 25°C. The components of the choline chloride solution contained 92 mM choline chloride, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 5 mM sodium ascorbate, 2 mM thiourea, 3 mM sodium pyruvate, 10 mM MgSO4.7H2O, 0.5 mM CaCl2.2H2O, and 12 mM N-acetyl-L-cysteine. Next, the post-digested cochlear samples were gently triturated using fire-polished glass Pasteur pipettes (13-678-20b; Fisher) with 4 different pore sizes (largest size the first, and smallest one the last). The picked endogenous IHCs and iOHCs were immediately subjected to reverse-transcription and cDNA amplification using a Smart-Seq HT kit (Cat# 634437, Takara).

value: Cochlea

tag: age

value: postnatal day 42

value: Slc26a5-CreER/+; Rosa26Tbx2/+


title: P42_cIHC-66


title: P42_cIHC-64


title: MOCK1

source_name: primary hepatocyte, BSA, 24hr, replicate 1


title: MOCK3

source_name: primary hepatocyte, BSA, 24hr, replicate 3


title: P42_cIHC-65


title: CD100-stimulated 1

source_name: primary hepatocyte,CD100, 24hr, replicate 1


title: L2C2: Spinal cord


title: L2C1: Spinal cord


title: P42_cIHC-63


title: L1A4: Spinal cord

value: Upper spinal cord


title: P42_cIHC-61


title: P42_cIHC-59


title: P42_cIHC-60


title: L1A2: Spinal cord


title: P42_cIHC-58


title: P42_cIHC-56


title: P42_cIHC-57


title: L1A1: Spinal cord


title: P42_cIHC-54


title: L1A3: Spinal cord


title: P42_cIHC-55


title: P42_cIHC-51


title: P42_cIHC-52


title: P42_cIHC-53


title: P42_cIHC-50


title: L1C4: Spinal cord


title: L1C2: Spinal cord


title: P42_cIHC-48


title: L1C3: Spinal cord


title: P42_cIHC-47


title: L2T4: Spinal cord

value: 23 days-post injury with training


title: P42_cIHC-44


title: P42_cIHC-62


title: L1C1: Spinal cord


title: L2T3: Spinal cord


title: P42_cIHC-43


title: P42_cIHC-45


title: P42_cIHC-46


title: P42_cIHC-42


title: L2T2: Spinal cord


title: P42_cIHC-41


title: L2T1: Spinal cord


title: P42_cIHC-40


title: P42_cIHC-39


title: P42_cIHC-37


title: P42_cIHC-38


title: L2N3: Spinal cord

value: 23 days-post injury without training


title: P42_cIHC-49


title: L2N2: Spinal cord


title: P42_cIHC-36


title: M4

city: hangzhou

first: Yumeng

last: Pei

state: zhejiang

address: Xihu district Zhuan Tang street

institute: Zhejiang university

data_processing:
Quality control were processed by Cutadapt(V1.9.1),  clean data were aligned to reference genome via software Hisat2 (v2.0.1), Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.Differential expression analysis used the DESeq2 Bioconductor package.
Assembly: mm10
Supplementary files format and content: excel file include fpkm for each sample

source_name: Intestinal organoid

growth_protocol: Theorganoids were embedded in Matrigel (Corning, 356231), and cultured in IntestiCult OGM medium(STEM CELL, 06005).

extract_protocol:
the intestine was cut into ~5 mm pieces and incubated with 5 mM EDTA-PBS at 4°C for 30 min. Following the incubation, the intestine was transferred to PBS and agitated vigorously. The supernatant was collected and filtered through 100-μm filter. The collection step was repeated 3 times. The combined cell suspension was filtered through 70-μm strainers and centrifuged at 300 x g for 5 min. The isolated crypts were embedded in Matrigel (Corning, 356231) at a density of approximately 100 crypts per μl and cultured in IntestiCult OGM medium (STEM CELL, 06005). For subculture and maintenance, the culture medium was replenished every two days, and the organoids were passaged at a 1:4 ratio every 5 days
Total RNA of each sample was extracted using TRIzol Reagent.

value: Intestinal organoid


title: 22RV1 cells, RBprotac-10 umol/L_3

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

description: 22RV1_cells_RBprotac__gene_fpkm_expression.txt

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: prostate

growth_protocol: 22RV1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: prostate

value: 22RV1 cells

value: prostate cancer cells

value: the treat group of inhibition of RB1 by RBprotac 10 umol/L

value: drug inhibition


title: M1


title: P42_cIHC-34


title: P42_cIHC-35


title: L2N1: Spinal cord

value: Sprague Dawley

value: Lower spinal cord


title: M3


title: P42_cIHC-33


title: 22RV1 cells, RBprotac-10 umol/L_1


title: P42_cIHC-31


title: WT3

value: wt


title: WT2


title: P42_cIHC-32


title: 22RV1 cells, RBprotac-10 umol/L_2


title: 22RV1 cells, RBprotac-5 umol/L_3

value: 22RV2 cells

value: the treat group of inhibition of RB1 by RBprotac 5 umol/L


title: WT4


title: P42_cIHC-30

value: Cochlea


title: 22RV1 cells, RBprotac-5 umol/L_2


title: P42_cIHC-29

value: postnatal day 42


title: L2N4: Spinal cord


title: M2


title: WT1


title: P42_cIHC-28

value: Slc26a5-CreER/+; Rosa26Tbx2/+


title: QGP-1/tet-MUC1shRNA_DOX+ Rep3

city: Brookline

first: Hiroki

last: Ozawa

address: 450 Brookline

institute: Dana-Farber Cancer Institute

description:
QGP-1 STAR_Gene_Counts.csv
QGP-1 STAR_Gene_TPM.csv
QGP1_DOXplus3

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: hg38
Supplementary files format and content: comma separated value file include raw counts for each sample
Supplementary files format and content: comma separated value file include TPM for each sample

source_name: pancreas

growth_protocol: QGP-1 cells were maintained in Gibco RPMI 1640 Media containing 10% heat inactivated FBS, 1% L-glutamine. BON-1 cells were maintained in Gibco Dulbecco’s Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F-12) containing 10% heat inactivated FBS and 2% L-glutamine.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

value: pancreas

value: pNET

value: DOX


title: 22RV1 cells, RBprotac-0 umol/L_3

value: the control group of inhibition of RB1 by RBprotac


title: 22RV1 cells, RBprotac-5 umol/L_1

value: prostate


title: P42_cIHC-27


title: QGP-1/tet-MUC1shRNA_DOX+ Rep1

description:
QGP-1 STAR_Gene_Counts.csv
QGP-1 STAR_Gene_TPM.csv
QGP1_DOXplus1


title: QGP-1/tet-MUC1shRNA_DOX+ Rep2

description:
QGP-1 STAR_Gene_Counts.csv
QGP-1 STAR_Gene_TPM.csv
QGP1_DOXplus2


title: QGP-1/tet-MUC1shRNA_DOX- Rep3

description:
QGP-1 STAR_Gene_Counts.csv
QGP-1 STAR_Gene_TPM.csv
QGP1_DOX-3

value: DMSO


title: 22RV1 cells, RBprotac-0 umol/L_2

value: 22RV1 cells

value: prostate cancer cells


title: 22RV1 cells, HA-RB(245-255)_3

description: 22RV1_cells_EV__RB(245-255)_gene_fpkm_expression.txt

value: the control group of overexpression of RB(245-255) by plasmids

value: transfection infection


title: P42_cIHC-26


title: P42_cIHC-24


title: 22RV1 cells, RBprotac-0 umol/L_1

value: drug inhibition


title: QGP-1/tet-MUC1shRNA_DOX- Rep1

description:
QGP-1 STAR_Gene_Counts.csv
QGP-1 STAR_Gene_TPM.csv
QGP1_DOX-1


title: BON-1/tet-MUC1shRNA_DOX+ Rep3

description:
BON-1 STAR_Gene_Counts.csv
BON-1 STAR_Gene_TPM.csv
BON_1_DOXp_3


title: 22RV1 cells, HA-RB(245-255)_2


title: P42_cIHC-23


title: P42_cIHC-22


title: 22RV1 cells, HA-RB(245-255)_1


title: BON-1/tet-MUC1shRNA_DOX+ Rep1

description:
BON-1 STAR_Gene_Counts.csv
BON-1 STAR_Gene_TPM.csv
BON_1_DOXp_1


title: 22RV1 cells, EV(245-255)_3


title: BON-1/tet-MUC1shRNA_DOX+ Rep2

description:
BON-1 STAR_Gene_Counts.csv
BON-1 STAR_Gene_TPM.csv
BON_1_DOXp_2


title: P42_cIHC-21


title: 22RV1 cells, EV(245-255)_2


title: P42_cIHC-20


title: BON-1/tet-MUC1shRNA_DOX- Rep3

description:
BON-1 STAR_Gene_Counts.csv
BON-1 STAR_Gene_TPM.csv
BON_1_DOXn_3


title: 22RV1 cells, HA-RBN_3

description: 22RV1_cells_EV_RBN_gene_fpkm_expression.txt

value: the treat group of overexpression of RBN by plasmids


title: P42_cIHC-19


title: BON-1/tet-MUC1shRNA_DOX- Rep2

description:
BON-1 STAR_Gene_Counts.csv
BON-1 STAR_Gene_TPM.csv
BON_1_DOXn_2


title: 22RV1 cells, HA-RBN_2


title: P42_cIHC-25


title: P42_cIHC-17


title: 22RV1 cells, EV(245-255)_1


title: 22RV1 cells, HA-RBN_1


title: BON-1/tet-MUC1shRNA_DOX- Rep1

description:
BON-1 STAR_Gene_Counts.csv
BON-1 STAR_Gene_TPM.csv
BON_1_DOXn_1


title: QGP-1/tet-MUC1shRNA_DOX- Rep2

description:
QGP-1 STAR_Gene_Counts.csv
QGP-1 STAR_Gene_TPM.csv
QGP1_DOX-2


title: C4-2 cells, trim24si-2

description: C4-2_cells__TRIM24_gene_count_expression.txt

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg38
Supplementary files format and content: The details of the data we process are in the linux terminal, first using trim_galore to trim the sequence reads of the header sequence/low quality sequence, then using hisat2 to map the trimmed sequence reads to hg38, and finally using featureCounts for read count extraction and normalization.

growth_protocol: C4-2 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

value: C4-2 cells

value: the treat group of knockdown of TRIM24 by siRNA


title: 22RV1 cells, EV(RBN)_3

value: the control group of overexpression of RBN by plasmids


title: C4-2 cells, trim24si-3


title: 22RV1 cells, EV(RBN)_2


title: C4-2 cells, trim24si-1


title: C4-2 cells, trim24nc-3

value: the control group of knockdown of TRIM24 by siRNA


title: P42_cIHC-15

value: Cochlea

value: postnatal day 42

value: Slc26a5-CreER/+; Rosa26Tbx2/+


title: P42_cIHC-14


title: 22RV1 cells, EV(RBN)_1


title: P42_cIHC-13


title: C4-2 cells, trim24nc-2


title: 22RV1 cells, siRB1_3

description: 22RV1_cells_siNC_siTRIM24_siRB1_gene_fpkm_expression.txt

value: the treat group of knockdown of RB1 by siRNA


title: P42_cIHC-16


title: P42_cIHC-12


title: C4-2 cells, trim24nc-1


title: 22RV1 cells, siRB1_2


title: C4-2 cells, RBsi-3

description: C4-2_cells__RB_gene_count_expression.txt


title: P42_cIHC-11


title: P42_cIHC-10


title: P42_cIHC-18


title: C4-2 cells, RBsi-2


title: 22RV1 cells, siRB1_1


title: 22RV1 cells, siTRIM24_3


title: C4-2 cells, RBsi-1


title: C4-2 cells, RBnc-1

value: the control group of knockdown of RB1 by siRNA


title: P42_cIHC-9


title: Pal_NC_IgG

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
CUTtag reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
CUTtag reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create CUTtag coverage plots, the locations of the mapped CUTtag reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
CUTtag libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: prostate

value: the control group of adding the effects of the Palbociclib

value: Drug effects


title: 22RV1 cells, siTRIM24_2

value: 22RV1 cells

value: prostate cancer cells


title: P42_cIHC-8


title: P42_cIHC-7


title: P42_cIHC-4


title: 22RV1 cells, siTRIM24_1

value: transfection infection


title: P42_cIHC-5


title: Day 0, IP, Retina, Replicate 6

city: Cambridge

first: William

middle: Jacob

last: Gammerdinger

state: MA

address: Massachusetts Hall

institute: Harvard University

data_processing:
Transcripts were quantified by a quasi-alignment approach using Salmon (version 1.6.0)
Assembly: mm10
Supplementary files format and content: Cobined counts data containing data from each sample

molecule: polyA RNA

source_name: Retina

growth_protocol: RNA was directly extracted from mouse retinal astrocytes from freshly ennucleated eyes

extract_protocol:
mRNA extraction was performed with oligo-dT beads and capturing poly(A) tails
cDNA library preparation was done with the Smart-Seq HT Ultra-low input RNA kit

treatment_protocol: RNA was isolated from untreated animals

value: Retina

tag: batch


title: 22RV1 cells, sicontrol_1

value: the control group of knockdown of TRIM24 and RB1 by siRNA


title: C4-2 cells, RBnc-2

value: C4-2 cells


title: C4-2 cells, RBnc-3


title: Pal_NC


title: P42_cIHC-3


title: P42_cIHC-2


title: Pal_add_IgG

value: the treat group of adding the effects of the Palbociclib


title: Pal_add


title: Day 0, IP, Retina, Replicate 5


title: Day 0, IP, Retina, Replicate 4


title: Sample 14_17H065

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Fastqs were processed by CellRanger version 5 with GEX fastq (samples 1-17) or GEX and ADT fastqs (pool of samples 18).
Sample 17 was multiplexed with other samples not part of the analysis, the FastQs pertaining to this sample were subsetted from the original FastQs
Filtered counts output from CellRanger are provided for samples 1-16 and 18 whereas raw counts are provided for sample 17.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: cell barcodes
Supplementary files format and content: features.tsv.gz: genes detected
Supplementary files format and content: matrix.mtx.gz: cell by gene expression matrix

source_name: Bone marrow

extract_protocol: 10X Chromium Single Cell 3'

value: Bone marrow

value: Primary acute myeloid leukemia cells

value: Female


title: P30_WT OHC-30

source_name: Wild type cochlear outer hair cells

value: Cochlea

value: postnatal day 30

value: Slc26a5-CreER/+; Ai9/+


title: Day 0, Input, Retina, Replicate 6


title: P30_WT OHC-29


title: P30_WT OHC-28


title: Sample 18_mixed 02H017, 03H112, 18H047

description: 02H017 (female); 03H112 (male); 18H047 (male)

value: 02H017 (KMT2A-rearranged); 03H112 (inv(16)); 18H047 (Complex karyotype)

value: pooled male and female


title: P42_cIHC-6

value: postnatal day 42

value: Slc26a5-CreER/+; Rosa26Tbx2/+


title: P30_WT OHC-27


title: Day 0, Input, Retina, Replicate 4


title: 22RV1 cells, sicontrol_3

value: prostate

value: 22RV1 cells


title: Sample 12_12H138

source_name: Peripheral blood

value: Peripheral blood

value: Complex karyotype


title: P30_WT OHC-31


title: 22RV1 cells, sicontrol_2

value: prostate cancer cells

value: the control group of knockdown of TRIM24 and RB1 by siRNA

value: transfection infection


title: Day 0, Input, Retina, Replicate 3

value: Retina


title: Sample 13_14H007

value: Primary acute myeloid leukemia cells

value: Normal karyotype


title: Day 0, IP, Retina, Replicate 2


title: Day 0, IP, Retina, Replicate 1


title: P30_WT OHC-32

value: Cochlea


title: Sample 11_12H106

value: Male


title: Sample 17_06H088

value: Bone marrow


title: P30_WT OHC-26

value: postnatal day 30

value: Slc26a5-CreER/+; Ai9/+


title: P30_WT OHC-25


title: Sample 9_11H103


title: Sample 8_11H097

value: Female


title: Day 0, Input, Retina, Replicate 1


title: Day 0, IP, Retina, Replicate 3


title: Day 0, Input, Retina, Replicate 5


title: P30_WT OHC-24


title: Day 0, Input, Retina, Replicate 2


title: Day 0, IP, ONP, Replicate 7

source_name: Optic Nerve Proper

value: Optic Nerve Proper


title: P30_WT OHC-23


title: Day 0, IP, ONH, Replicate 7

source_name: Optic Nerve Head

value: Optic Nerve Head


title: Sample 5_09H010


title: Sample 10_12H010


title: P42_cIHC-1

value: postnatal day 42

value: Slc26a5-CreER/+; Rosa26Tbx2/+


title: P30_WT OHC-21


title: P30_WT OHC-20


title: Sample 4_08H087


title: Day 0, IP, ONP, Replicate 6


title: P30_WT OHC-22


title: Sample 3_07H134

value: Peripheral blood


title: Day 0, IP, ONP, Replicate 4


title: P30_WT OHC-18


title: DEF_rep3

city: Los Angeles

last: Hurrell

state: CA

address: 1450 Biggy Street

institute: USC

data_processing:
Partek Flow, version 10.0
Sequence reads were trimmed by quality score (min Phred score 20 from both end, and trimmed reads shorter than 25bp were discarded).
Trimmed reads were mapped to mm10 with GENECODE M25 annotation as a guidance by STAR 2.7.8.
Aligned reads were further quantified to GENCODE M25 with Partek E/M algorithm.
Genes with less than 10 counts in all samples were removed from the analysis. The remaining genes were subjected to differential expression analysis by DESeq2 with median ratio normalization
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw read counts per gene per sample

source_name: lung

growth_protocol: Cells were freshly isolated on day 4 from the lungs of mice treated for 3 consecutive days with  0.5µg rmIL-33 intranasally and cultured for 18 hours with or without DEF with or without FeCl3 for an additional 8 hours.

extract_protocol:
Cultured ILC2s were recovered, lysed in RLT buffer (Qiagen) and RNA was extracted using the MicroRNeasy kit (Qiagen)
For each sample, a total of 10pg of RNA was used to generate cDNA (SMARTer Ultra Low Input RNA v3 kit, Clontech) for library preparation

treatment_protocol: DEF (500µM) and FeCl3 (200µM) were used as treatments for the indicated times. Vehicle was ddH2O.

value: lung

value: BALB/c

value: DEF


title: DEF_rep2


title: Sample 2_05H066


title: DEF+FeCl3_rep1

value: DEF + FeCl3


title: DEF_rep1


title: Sample 1_05H034

value: Primary acute myeloid leukemia cells


title: Sample 7_09H070

value: Normal karyotype


title: DEF+FeCl3_rep2


title: Day 0, IP, ONP, Replicate 2


title: Day 0, IP, ONP, Replicate 3


title: Sample 6_09H032


title: vehicle_rep3

value: vehicle


title: Colonoid 82C, EspP

city: Albuquerque

first: Julie

middle: Goeun

last: In

state: NM

address: 915 Camino de Salud, IDTC 3270

institute: University of New Mexico

description: 10X chromium

data_processing:
Raw FASTQ reads from sequencing were processed using Cell Ranger (V2.0.0) software from 10x genomics. Sequencing reads were demultiplexed, unique molecular identifier (UMI) were collapsed and reads aligned to 10X human transcriptome GRCh38-3.0.0 as the reference.
The raw data created by Cell Ranger was read into the Seurat R package for quality control and downstream processing. Low quality cells expressing <200 genes and genes expressed in fewer than 3 cells were filtered out. After looking at the violin plots of the number of counts, features (genes), and percent mitochondria per sample, we further filtered cells expressing >2000 genes in control samples and cells expressing >75000 genes in UBD treated samples to avoid probable doublets. Cells expressing >20% of mitochondrial genes were filtered out in control and UBD samples. To account for differences in sequencing depth across samples the data was log-normalized and scaled.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated value files and matrix files

source_name: proximal colon

growth_protocol: Human colonoids were maintained in Matrigel (phenol red-free, growth factor-reduced) in 24-well plates with high WNT3A/RSPO1/Noggin conditioned media, supplemented with EGF, B27

extract_protocol:
Colonoids were removed from Matrigel by incubation with organoid harvesting solution at 4°C for 30’, washed in Advanded DMEM and pelleted by centrifugation at 300 xg for 10’. Colonoids were resuspended in 500µl TrypLE enzyme solution, then transferred to a 24 well plate and spun at 600rpm at 32°C for 45’ in a spinoculator to digest into single cells. Single cells were washed in 10 ml of Advanced DMEM, pelleted again and resuspended in 1 ml of organoid media and filtered using 40 µm filters.
Using the Cell Countess II FL, single cell suspensions are observed. 10 µl of Trypan Blue was mixed with 10 µl of the cell suspension. 10 µl of the mixture was added to the disposable slide and the cell suspension observed for concentration and cell viability. The numbers recorded were used to determine how much of the cell suspension is to be used to start the 10x Chromium Next GEM protocol. Once those numbers are determined the Next GEM Chip G was loaded and put into the Chromium Controller for processing, creating the GEMs. After this step the GEMs were transferred into PCR tubes and cDNA Synthesis was completed per the 10X Chromium Next GEM 3' Protocol. After the cDNA was completed, it was processed on a DNA High Sensitivity Chip on the Agilent BioAnalyzer Machine to check that the cDNA processed correctly. Next the cDNA was fragmented, adaptor ligated and sample Indexed (Barcoded) with PCR. Once the libraries were completed they were processed on a DNA High Sensitivity Chip with the Agilent BioAnalyzer to ensure that the final libraries were approximately 500 bp in size. They were also processed with the KAPA Library Quantification Kit to verify the concentration of final libraries.

treatment_protocol: 50 ug/ml UBD or 10 ug/ml EspP  was added to colonoids in 50% v/v Matrigel for overnight (~18h) treatment

value: proximal colon

value: dissociated colonoids

value: African-American female, 67 years old

value: EspP


title: DEF+FeCl3_rep3


title: Day 0, IP, ONP, Replicate 1


title: P30_WT OHC-16

value: Cochlea

value: postnatal day 30

value: Slc26a5-CreER/+; Ai9/+


title: vehicle_rep2


title: P30_WT OHC-15


title: Day 0, IP, ONH, Replicate 5

value: Optic Nerve Head


title: Day 0, IP, ONH, Replicate 6


title: Colonoid 4C, EspP

description: 10X chromium

value: Hispanic male, 70 yrs old


title: scRNA_somitic_gastruloids_Zeb2_dTAG13

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
Raw sequencing data was processed using Cell Ranger (v6.1.2, 10x Genomics)
Assembly: mm10
Supplementary files format and content: barcode.tsv, features.tsv and matrix.mtx

source_name: E14_triple reporter

growth_protocol: Somitic gastruloids were generated as previously described (van den Brink et al., Nature 2020). Briefly, 300 single cells were FACS sorted with a BD FACSMelody™ cell sorter into U-bottomed 96 wells (Greiner Bio-one; 650185) containing 40μL NDiff227 (Takara). After 48h, the aggregates were treated with 3μM CHIR99021 (Axon 1386) and medium was refreshed every day with pre-equilibrated NDiff227. At 96h, four gastruloids were transferred with a P1000 pipette with the tip cut-off to 1.5mL Eppendorf tubes and resuspended in 10% Matrigel (Corning, 356231) and transferred to a 48-well Greiner Bio-one; 677180). For degradation of Zeb2, 100nM dTAG-13 was added to culture medium at 72h and 96h.

extract_protocol:
Gastruloids (~32) were harvested from matrigel with icecold PBS and spun down at 300xg for 5 min at 4°C. Gastruloids were trypsinized for 5 min at 37°C and resuspended in DMEM supplemented with 15% FBS. Cells were washed with cold PBS and resuspended in PBS containing 7-AAD and 0.04% BSA. Live cells were sorted at 4°C with a BD FACSMelody™ cell sorter in DNA LoBind tubes containing PBS with 0.04% BSA and centrifuged at 300xg for 5 min. Per sample, 10,000 cells were processed using the 10x Genomics Chromium Controller and the Chromium Single Cell 3’ Reagent kit (v3.1 Chemistry) following the standard manufacturer’s protocol.
ingle cell RNA sequencing libraries were generated using the Chromium Single Cell 3’ Reagent kit (v3.1 Chemistry) following the standard manufacturer’s protocol (10x genomics). The resulting libraries were sequenced on an Illumina Nextseq500 (1x 28bp + 1x56bp + 1x8bp index).

value: E14_triple reporter

value: somitic gastruloids

value: endogenous Zeb2-HA-FKBP12F36V degron tag

tag: assay

value: scRNA-seq


title: Colonoid 75C, EspP

description: 10X chromium

value: White male, 58 years old


title: P30_WT OHC-14


title: Colonoid 82C, metals

description: 10X chromium

value: uranium-bearing dust


title: P30_WT OHC-17


title: Day 0, IP, ONH, Replicate 3


title: Day 0, IP, ONH, Replicate 4


title: P30_WT OHC-13


title: P30_WT OHC-12


title: Day 0, IP, ONH, Replicate 2


title: scRNA_somitic_gastruloids_Zeb2_untreated


title: Colonoid 75C, metals

description: 10X chromium


title: RNAseq_somitic_gastruloids_dTAG13_2

data_processing:
Sequence reads were processed using the seq2science pipeline (v0.7.1, https://github.com/vanheeringen-lab/seq2science). In short, paired-end reads were trimmed with fastp (v0.20.1, default settings) and aligned with STAR (v2.7.6a, default settings) to the Mus musculus genome assembly GRCm38.p6. Aligned reads were filtered based on a minimum mapping quality of 255 and duplicate reads and reads in the ENCODE blacklisted regions were filtered out. Sample sequencing strandedness was inferred using RSeQC (v4.0.0) and number of reads per gene were measured with HTSeq count (v0.12.4). Deseq2 (v1.34.0) was used for downstream analysis.
Assembly: mm10
Supplementary files format and content: counts

growth_protocol: Somitic gastruloids were generated as previously described (Protoc. Exch. https://doi.org/10.1038/protex.2018.094, van den Brink et al., Nature 2020). Briefly, 300 single cells were FACS sorted with a BD FACSMelody™ cell sorter into U-bottomed 96 wells (Greiner Bio-one; 650185) containing 40μL NDiff227 (Takara). After 48h, the aggregates were treated with 3μM CHIR99021 (Axon 1386) and medium was refreshed every day with pre-equilibrated NDiff227. At 96h, gastruloids were transferred with a P1000 pipette with the tip cut-off to 1.5mL Eppendorf tubes and resuspended in 10% Matrigel (Corning, 356231) and transferred to a 48-well Greiner Bio-one; 677180). For degradation of Zeb2, gastruloids were treated with 100nM dTAG-13 (Tocris Biosciences) at 72 and 96h. DMSO was used as control.

extract_protocol:
RNA was extracted using Quick-RNA MicroPrep kit (Zymo Research) according to the manufacturer’s instruction with DNAseI treatment included.
For RNA-seq, libraries were generated from 250-500ng RNA with the KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems). Fragmentation and priming were performed at 94°C for 6 min. NEXTflex DNA barcodes were used for adaptor ligation. Libraries were amplified with 6-10 PCR cycles followed by a two steps library amplification cleanup using a 0.8x bead-based cleanup and then an 1x bead cleanup.

value: RNA-seq


title: Colonoid 4C, metals

description: 10X chromium


title: P30_WT OHC-11


title: Colonoid 82C, control

description: 10X chromium

value: control


title: P30_WT OHC-10


title: Day 0, IP, ONH, Replicate 1


title: RNAseq_somitic_gastruloids_dTAG13_1


title: vehicle_rep1

value: lung

value: BALB/c

value: vehicle


title: Colonoid 75C, control

description: 10X chromium

value: proximal colon

value: dissociated colonoids


title: Old Tom+ HSC rep2

city: Santa Cruz

first: Camilla

last: Forsberg

address: 1156 High Street

institute: Institute for the Biology of Stem Cells, University of California Santa Cruz

data_processing:
Paired-end Illumina reads were trimmed to 75x75bp.
Bowtie2 was used to filter reads for the mouse genome.
STAR was used to map to mm10 assembly
DESeq  was used to perform differential expression analysis
Assembly: mm10
Supplementary files format and content: DESeq results for genes analyzed comparing the mkpy replicates to the mkpo replicates.

growth_protocol: Flt3-cre mice were crossed to mTmG mice and offspring were aged to 3 months (young) or 20 months old (old)

extract_protocol:
Total RNA was isolated from sorted  using trizol and following manufacturers instructions
RNA-seq libraries  were prepared using NEBNext® Ultra kit (New England Biolabs, using Tn5) following manufacturer instructions

treatment_protocol: Bone Marrow cells were stained with fluorescent antibodies, and Tom+ or GFP+ fractions of Lin-cKit+Sca1-CD150+CD41+ cells, and Lin-cKit+Sca+-CD150+Flk2-Tom+ cells were isolated by flow cytometry

value: Bone marrow

value: male

value: Hematopoeitic Stem Cell

value: old, 18-20 month


title: P30_WT OHC-9

value: Cochlea

value: postnatal day 30

value: Slc26a5-CreER/+; Ai9/+


title: RNAseq_somitic_gastruloids_untreated_1

value: E14_triple reporter

value: somitic gastruloids

value: endogenous Zeb2-HA-FKBP12F36V degron tag


title: Old Tom+ HSC rep1


title: P30_WT OHC-8


title: ChIP_Zeb2_gastruloids_2

data_processing:
Sequence reads were processed using the seq2science pipeline (v0.7.1, https://github.com/vanheeringen-lab/seq2science). Briefly, paired-end reads were trimmed with fastp (v0.20.1, default settings) and aligned with bwa-mem2 (v2.2.1, options ‘-M’) to the Mus musculus genome assembly GRCm38.p6. Aligned reads were filtered based on mapping quality (MAPQ ≥ 30) and filtering out duplicate reads and reads in the ENCODE blacklisted regions. Peaks were called with MACS2 (v2.2.7) with default settings in BAMPE mode. The peaks called in both replicates were used for analysis.
Assembly: mm10
Supplementary files format and content: narrowPeak

growth_protocol: The dual BRA-GFP (Brachyury), SOX17-RFP reporter mouse ES cell line (Pour et al., 2022 ) was cultured on 0.15% (w/v) gelatin-coated dishes in Dulbeccco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 15% fetal bovine serum (FBS, HyClone), 2mM GlutaMAX (Gibco), non-essential amino acids (Gibco), 50U/mL penicillin-streptomycin (Gibco), 100µM β-mercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house).  Gastruloids were generated as previously described (Protoc. Exch. https://doi.org/10.1038/protex.2018.094, van den Brink et al., Nature 2020). Briefly, 300 single cells were FACS sorted with a BD FACSMelody™ cell sorter into U-bottomed 96 wells (Greiner Bio-one; 650185) containing 40μL NDiff227 (Takara). After 48h, the aggregates were treated with 3μM CHIR99021 (Axon 1386) and medium was refreshed every day with pre-equilibrated NDiff227.

extract_protocol:
Ttrypsinized gastruloids were crosslinked in solution A with 2mM disuccinimidyl glutarate (Thermo Fisher Scientific #20593) for 25 min, followed by 1% formaldehyde methanol-free (Thermo Fisher Scientific, #28906) for 20 min. Chromatin extracts were sonicated for 2-4 cycles of 30 sec on, 30 sec off using a Diagenode Bioruptor Pico. For each ChIP, 4µg of V5 Tag antibody (Thermo Fisher Scientific, #R960CUS) or 4µg of HA antibody (a mix of 2µg from Roche 11867423001 and 2µg from Invitrogen 71–5500) was pre-conjugated to 40ul of Protein A/G magnetic beads (Invitrogen).
Immunoprecipitated DNA was processed for library preparation using the Kapa HyperPrep Kit (Kapa Biosystems) and barcoded with NEXTflex DNA barcode.

tag: chip antibody

value: HA

value: gastruloids

value: ChIP-seq


title: Stage_IV_Steady_State_3

city: Liege

last: Desmet

address: B34, Avenue de l'Hopital 1

institute: University of Liege

data_processing:
Sequenced reads were aligned and mapped to the human genome (UCSC hg19) with RNA-Seq Alignment (Version:2.0.2) using STAR_2.6.1a on BaseSpace (https://basespace.illumina.com).
Normalization and analysis of the obtained data was performed using DESeq2 R package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Assembly: human genome (UCSC hg19)
Supplementary files format and content: Tab-delimited file describing the number of reads mapped to each gene as obtained with RNA-Seq Alignment (Version:2.0.2) on BaseSpace (https://basespace.illumina.com).

source_name: Bone Marrow

extract_protocol:
For every mL of TRIzol, 200uL of chloroform was added, and the samples were vigorously mixed and incubated for 2 minutes at room temperature. Samples were centrifuged at 10,000xg for 15 minutes at 4°C to separate the phases. The RNA-containing upper aqueous phase was transferred to a new microcentrifuge tube containing 475uL of isopropanol and 2uL of glycoblue (ThermoFisher, AM9515). Samples were centrifuged at 10,000xg for 15 minutes and supernatant was discarded. One volume of 75% ethanol was added and samples were centrifuged at 10,000xg for 1 minute to precipitate the RNA and discard the supernatant. RNA pellet was resuspended in 40uL of DNase/RNase-free water for a 15-minute DNase treatment (Zymo Research, E1010). DNase treatment was followed by column-based RNA purification with the RNA Clean & concentrator-5 kit (Zymo Research, R1016). Briefly, 100uL of RNA binding buffer was added to every 50µL sample and mixed thoroughly. One volume of 100% ethanol was added and the sample was transferred into a Zymo-Spin IC column in a collection tube. Columns were centrifuged at 10,000xg for 30 seconds and flow-through was discarded. The column was washed once with RNA prep buffer and twice with RNA wash buffer, following the manufacturer’s instructions. RNA was eluted in 10uL of DNase/RNase-free water. Purified RNA integrity and quantity was assessed using the RNA 6000 Pico kit (Agilent) for the presence of 18s and 28s rRNA peaks.
Full length cDNA was prepared from isolated RNA using SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio, 634889) following the manufacturer's instructions, with 17 cycles of cDNA amplification. Final cDNA quality was assessed using Agilent High Sensitivity DNA kit (Agilent, 5067-4626). cDNA libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina, FC-131-1024) using the manufacturer’s instructions.

treatment_protocol: Single cell suspensions of human bone marrow were first stained with Lineage-cocktail (BioLegend, 348801) for 30 minutes on ice. Samples were immunomagnetically enriched for cells of interests using EasySep™ FITC positive selection kit II (Stemcell, 17682) as described in the manufacturer’s instructions. The negative fractions were next stained for CD84-BV421 (BD Biosciences, 566904), FcεR1α-BV510 (BD Biosciences, 747786), CD11b-BV711 (BioLegend, 101242), CD45-BV786 (BD Biosciences, 563204), Siglec-8-BB700 (BD Biosciences, 747867), CD38-PE (BioLegend, 356604), CD200R-PE-cy7 (BioLegend, 329312), CCR3-APC (Miltenyi, 130-123-300), and CD66b-APC-cy7 (BioLegend, 305126) in 1X BD Horizon™ Brilliant stain buffer (BD Biosciences, 563794) for 30 minutes at room temperature. Cell suspensions were washed twice and resuspended in PBS supplemented with 5nM BD Via-Probe™ Green (BD Biosciences, 565802). Four maturation stages of eosinophils were sorted directly into TRIzol (ThermoFisher, 15596026) or into FACS buffer for bright-field microscopy using a BD FACSAria III (BD Biosciences) cell sorter with a 100μm nozzle. Sort purity was at 95 per cent or higher and samples were stored at -80°C for downstream RNA applications.

tag: tissue

value: Bone Marrow

value: Bone marrow eosinophil developmental stages

value: steady state


title: Old Tom+ MkP rep 2

value: Megakaryocyte Progenitor


title: RNAseq_somitic_gastruloids_untreated_2

tag: cell line

value: RNA-seq


title: Stage_II_Steady_State_3

tag: cell type


title: Stage_III_Steady_State_3


title: ChIP_Zeb2_gastruloids_1

tag: genotype


title: P30_WT OHC-6


title: ChIP_Sp5_gastruloids_1

value: endogenous Sp5-HA-FKBP12F36V degron tag


title: P30_WT OHC-4


title: ChIP_Sp5_gastruloids_2


title: Old GFP+ MkP rep 1

value: Bone marrow

value: male

tag: treatment


title: P30_WT OHC-19

value: Cochlea


title: ChIP_Rxrα_gastruloids_2

value: endogenous Rxr[alpha]-HA-FKBP12F36V degron tag


title: Old Tom+ MkP rep 1

tag: Sex

value: old, 18-20 month


title: Stage_I_Steady_State_3


title: Young GFP+ MkP rep 3

value: young, 3 month


title: P30_WT OHC-3

tag: strain

value: postnatal day 30

value: Slc26a5-CreER/+; Ai9/+


title: Stage_IV_Steady_State_2


title: ChIP_Rxrα_gastruloids_1

value: HA

value: E14_triple reporter


title: Colonoid 4C, control

description: 10X chromium

value: proximal colon

value: dissociated colonoids

value: Hispanic male, 70 yrs old

value: control


title: Young GFP+ MkP rep 2

value: Megakaryocyte Progenitor


title: Stage_III_Steady_State_2

value: Bone Marrow

value: Bone marrow eosinophil developmental stages

value: steady state


title: P30_WT OHC-2


title: P30_WT OHC-1


title: Young GFP+ MkP rep 1

value: Bone marrow

value: male


title: Stage_II_Steady_State_2


title: P30_WT OHC-5

value: Cochlea


title: Old GFP+ MkP rep 2

value: old, 18-20 month


title: Stage_I_Steady_State_2


title: Stage_IV_IL33_Induced_Eosinophilia_3

data_processing:
Sequenced reads were aligned and mapped to the mouse genome (mm10) with RNA-Seq Alignment (Version:2.0.2) using STAR_2.6.1a on BaseSpace (https://basespace.illumina.com).
Normalization and analysis of the obtained data was performed using DESeq2 R package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Assembly: mm10
Supplementary files format and content: Tab-delimited file describing the number of reads mapped to each gene as obtained with RNA-Seq Alignment (Version:2.0.2) on BaseSpace (https://basespace.illumina.com).

extract_protocol:
For every mL of TRIzol, 200uL of chloroform was added, and the samples were vigorously mixed and incubated for 2 minutes at room temperature. Samples were centrifuged at 10,000xg for 15 minutes at 4°C to separate the phases. The RNA-containing upper aqueous phase was transferred to a new microcentrifuge tube containing 475uL of isopropanol and 2uL of glycoblue (ThermoFisher, AM9515). Samples were centrifuged at 10,000xg for 15 minutes and supernatant was discarded. One volume of 75% ethanol was added and samples were centrifuged at 10,000xg for 1 minute to precipitate the RNA and discard the supernatant. RNA pellet was resuspended in 40uL of DNase/RNase-free water for a 15-minute DNase treatment (Zymo Research, E1010). DNase treatment was followed by column-based RNA purification with the RNA Clean & concentrator-5 kit (Zymo Research, R1016). Briefly, 100uL of RNA binding buffer was added to every 50L sample and mixed thoroughly. One volume of 100% ethanol was added and the sample was transferred into a Zymo-Spin IC column in a collection tube. Columns were centrifuged at 10,000xg for 30 seconds and flow-through was discarded. The column was washed once with RNA prep buffer and twice with RNA wash buffer, following the manufacturer’s instructions. RNA was eluted in 10uL of DNase/RNase-free water. Purified RNA integrity and quantity was assessed using the RNA 6000 Pico kit (Agilent) for the presence of 18s and 28s rRNA peaks.
Full length cDNA was prepared from isolated RNA using SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio, 634889) following the manufacturer's instructions, with 17 cycles of cDNA amplification. Final cDNA quality was assessed using Agilent High Sensitivity DNA kit (Agilent, 5067-4626). cDNA libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina, FC-131-1024) using the manufacturer’s instructions.

treatment_protocol: Single cell suspensions of murine bone marrow were pooled from 3 CB57BL/6 donor mice in the steady state or from 3 mice that received daily intraperitoneal injections of 400 ng recombinant murine IL-33 for 7 days were first stained for Ly6G-FITC (BioLegend, 127606), CD90.2-FITC (BioLegend, 140204), NK1.1-FITC (eBioscience, 11-5941-85), CD45R-FITC (eBioscience, 11-0452-85) for 30 minutes on ice. Samples were immunomagnetically enriched for cells of interest using EasySep™ FITC positive selection kit II (Stemcell, 17682) as described by the manufacturer’s instructions. The negative fractions were subsequently stained for CD29-pacblue (BioLegend, 102224), F4/80-BV510 (BioLegend, 123125), Siglec-F-BV711(BD Biosciences,740764), CD55-biotin-streptavidin-BV786(R&D, BAF5376, BD Biosciences, 563858), CD117-BB700 (BD Biosciences, 566414), Pir-A/B-PE (BioLegend, 144104) and CD200R3-PE-cy7 (BioLegend, 142212) in 1X BD Horizon™ Brilliant stain buffer (BD Biosciences, 563794) for 30 minutes on ice. Cell suspensions were washed twice and resuspended in PBS supplemented with 5nM BD Via-Probe™ Green (BD Biosciences, 565802). cells in each of the four stages of eosinophil maturation were sorted directly into TRIzol (ThermoFisher, 15596026) using a BD FACSAria III (BD Biosciences) cell sorter with a 100μm nozzle. Sort purity was at 95 per cent or higher and samples were stored at -80°C for downstream RNA applications.

value: wild type

value: IL-33 induced eosinophilia


title: Stage_IV_Steady_State_1


title: P30_WT OHC-7

value: postnatal day 30

value: Slc26a5-CreER/+; Ai9/+


title: blau1RTmela

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.17.1.14
STAR version 2.5.2a was used to align the reads to the hg38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in hg38 version 97
Assembly: hg38 version 97
Supplementary files format and content: Tab-delimited gene counts

source_name: tumor xenograft

extract_protocol:
Trizol reagent
TruSeq RNA Library Prep Kit v2 (Illumina)

value: tumor xenograft

value: human melanoma

value: systemic treatment with anle138b


title: Stage_III_Steady_State_1

first: Christophe


title: Stage_III_IL33_Induced_Eosinophilia_3


title: Stage_II_IL33_Induced_Eosinophilia_3


title: 5L-Juni2018-cont

value: no treatment


title: ChIP_p300_gastruloids_1

value: E14_triple reporter

value: gastruloids

value: endogenous p300-V5-miniTurboID

value: ChIP-seq


title: Stage_II_Steady_State_1

value: Bone Marrow

value: Bone marrow eosinophil developmental stages

value: steady state


title: 4L-Juni2018-cont


title: Stage_I_Steady_State_1


title: ChIP_Rxrα_mESCs_2

value: HA

value: mESCs

value: endogenous Rxr[alpha]-HA-FKBP12F36V degron tag


title: Stage_IV_IL33_Induced_Eosinophilia_2

value: wild type

value: IL-33 induced eosinophilia


title: Stage_I_IL33_Induced_Eosinophilia_3


title: 3R-Juni2018-exp


title: ChIP_p300_mESCs_2


title: input_gastruloids

value: input


title: ChIP_Rxrα_mESCs_1


title: ChIP_p300_mESCs_1


title: 2R-Juni2018-exp

value: tumor xenograft


title: Donor4_Stimulated_DMSO_vehicle_Day6

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

description:
150-bp paired end seq
104295-001-016

data_processing:
FastQC v0.11.9 was used to check raw reads, and Cutadapt v2.10 to perform adapter clipping.
Reads are mapped to a reference genome (Ensembl gene annotation v102, GRCh38) using STAR aligner v2.7.5a.
After removing PCR duplicates detected by UMI with umitools v0.5.5, HTSeq Count v0.12.4 was used for counting of aligned reads.
Assembly: GRCh38
Supplementary files format and content: TSV, gene count table

source_name: Sorted B-cells from healthy control

growth_protocol: Blood PBMC's were isolated using ficoll density gradient centrifugation, subsequently thawed and FACS sorted for naïve B-cells (CD20+CD27-IgG-IgA-)

extract_protocol:
GenElute Mammalian Total RNA kit (Sigma-Aldrich) or RNeasy Micro Kit (Qiagen)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), performed by GenomeScan B.V.

treatment_protocol: 3 to 6 day culture in medium containing IL10, IL21, anti-IgM and CD40L, with or without either ATM-inhibitor or DNA-PK-inhibitor.

value: Cultured cells

value: Stimulated Naive B-cells

value: Healthy Control

value: DMSO

tag: time point


title: blau5RTcontr

value: human melanoma

value: no treatment


title: Donor4_Unstimulated_Day0

description:
150-bp paired end seq
104295-001-021

value: Sorted Naive B-cells


title: PANC-1 cells, IKE treated, bioreplicate 4: Ribo-seq

first: Dan

last: Su

address: No. 1 Shuaifuyuan, Wangfujing Street, Beijing

department: Department of General Surgery

institute: Peking Union Medical college hospital

description:
ribosome-protected fragments (RPFs)
PANC-IKE-4

data_processing:
Sequencing reads from Ribo-seq were first filtered by fastp to remove low-quality reads, and then filtered using the short reads alignment tool Bowtie2 (version 2.2.8) to further remove reads that were mapped to ribosome RNA (rRNA), transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), and miRNA.
The sequencing reads were mapped to human genome by STAR software and then quantified using the RSEM software by calculating the FPKM (fragment per kilobase of transcript per million mapped reads) values.
Differential expression analysis was performed using DESeq2 software
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes FPKM values of each sample
Library strategy: Ribo-seq

growth_protocol: PDAC cells were cultured with Dulbecco’s modified Eagle’s medium (DMEM, Viacell),  or Iscove's Modified Dulbecco's Medium (IMDM, Viacell), which were supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 1% normocin (Invivogen), at 37 °C in a humidified incubator containing 5% CO2

extract_protocol:
PDAC cells (CFPAC-1 and PANC-1) were treated with 0.1% DMSO or IKE for five consecutive days and then incubated with 100 μg/mL CHX at 37 °C for 2 min to terminate the movement of ribosomes along mRNAs. Cells were then wash twice with ice-cold PBS containing 100 μg/mL CHX to remove dead cells and cell debris, and scratched off in ice-cold PBS containing 100 μg/mL CHX to collect survived PDAC cells. After centrifugation, the cell pellets were resuspended in polysome lysis buffer (20 mM HEPES (pH 7.4), 100 mM KCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 μg/mL cycloheximide), incubated on ice for 10 min, triturated ten times through a 26-G needle, and centrifuged at 20000g for 10min at 4℃ to collect supernatants. To prepare ribosome-protected fragments (RPFs), RNase I (NEB, Ipswich, MA, USA) and DNase I (NEB, Ipswich, MA, USA) were added into cell lysates to digest the free RNAs and the nuclease digestion reaction was kept for 45 min at RT with gentle mixing. Isolation of RPFs with a size greater than 17nt was achieved by size-exclusion chromatography with MicroSpin S-400 HR columns (GE Healthcare, USA) and RNA Clean and Concentrator-25 kit (Zymo Research; R1017) following the instructions of the manufacturer.
After removing contaminating rRNA, the recovered RPFs were then applied for library construction using NEBNext® Multiple Small RNA Library Prep Set for Illumina®

treatment_protocol: CFPAC-1 and PANC-1 cells were treated with 10 μM or 1 μM  IKE (imidazole ketone erastin, a derivative of erastin) for 24 h. PDAC cells treated with 0.1% DMSO were used as a parallel control.  After removing dead cells and cell debris, survived PDAC cells were collected for sequencing analysis.

value: pancreatic adenocarcinoma cells

value: 1 microM IKE,24 h


title: Stage_II_IL33_Induced_Eosinophilia_2

value: Bone Marrow

value: Bone marrow eosinophil developmental stages


title: ChIP_p300_gastruloids_2

value: E14_triple reporter

value: gastruloids

value: endogenous p300-V5-miniTurboID

value: ChIP-seq


title: Donor3_Unstimulated_Day0

description:
150-bp paired end seq
104295-001-020


title: Stage_I_IL33_Induced_Eosinophilia_2

value: wild type

value: IL-33 induced eosinophilia


title: PANC-1 cells, IKE treated, bioreplicate 3: Ribo-seq

description:
ribosome-protected fragments (RPFs)
PANC-IKE-3


title: scAIR001: scRNA-seq

city: Shenzhen

first: Tian

last: (Simon) Zhongyuan

state: Guangdong

address: 1088 Xueyuan Avenue

department: School of Life Sciences

institute: Southern University of Science and Technology (SUSTech)

description: 10x Genomics

data_processing:
Raw sequencing data from scAIR are divided into 5 FASTQs: For scRNA-seq: (1) R1 corresponds to the cell barcode; (2) R2 corresponds to the sequencing reads from the cDNA molecule. For scATAC-seq: (1) R1 and R3 refer to the squencing reads from the DNA fragment; (2) R2 refers to the cell barcode.
Assembly: dm3
Supplementary files format and content: scRNA seq Matrix, scATAC seq Pairs
Library strategy: scAIR

organism: Drosophila melanogaster

source_name: Embryos nuclei

growth_protocol: To culture fruit flies for obtaining embryonic tissues, prepare a nutrient-rich culture medium by mixing cornmeal, yeast, sugar, and water. Transfer the fruit flies to vials containing the culture medium and seal them. Maintain the vials in a controlled environment with a 12-hour light-dark cycle. Allow the fruit flies to mate and lay eggs on the surface of the culture medium. After a few days, transfer the contents of the vials to a Petri dish. Use a stereomicroscope to collect the tiny embryos after 24 hours.

extract_protocol:
Crosslinked cells were initially subjected to cell lysis and nuclei lysis to extract the nuclei. The lysed nuclei were then fragmented into smaller complexes using restriction enzymes, which cut the DNA at specific recognition sites. Following fragmentation, proximity ligation was performed to join the fragmented DNA ends together. This step helps generate smaller DNA fragments with proximity ligation, allowing for easier sequencing. The ligated nuclei were subsequently uploaded to the 10x Genomics platform for further processing and analysis.
The barcoded RNA and DNA by 10x genomics were performed library construction following the manual.

treatment_protocol: After collecting the eggs laid by adult female fruit flies, the embryos are carefully separated from the eggshell and transferred to a microcentrifuge tube. A lysis buffer is added to break down the cell membranes and release the nuclei. The embryos are gently squashed to further disrupt the cells, and the resulting mixture is centrifuged to separate the nuclei from cellular debris. The isolated nuclei are then subjected to crosslinking, a process that helps stabilize the nuclear proteins and DNA interactions

value: Embryos nuclei

tag: developmental stage


title: Donor1_Unstimulated_Day0

description:
150-bp paired end seq
104295-001-019

value: Cultured cells


title: scAIR001: scATAC-seq and interactome

description: 10x Genomics


title: input_mESCs

value: input

value: mESCs


title: PANC-1 cells, IKE treated, bioreplicate 2: Ribo-seq

description:
ribosome-protected fragments (RPFs)
PANC-IKE-2


title: Donor4_Stimulated_ATM-inhibitor_Day6

description:
150-bp paired end seq
104295-001-018

value: Stimulated Naive B-cells

value: Healthy Control

value: ATM-inhibitor


title: Stage_IV_IL33_Induced_Eosinophilia_1


title: PANC-1 cells, IKE treated, bioreplicate 1: Ribo-seq

description:
ribosome-protected fragments (RPFs)
PANC-IKE-1

value: pancreatic adenocarcinoma cells


title: Stage_III_IL33_Induced_Eosinophilia_1


title: Stage_II_IL33_Induced_Eosinophilia_1


title: Donor4_Stimulated_DNA-PKinhibitor_Day6

description:
150-bp paired end seq
104295-001-017

value: DNA-PKinhibitor


title: RNA-seq Ctrl

data_processing:
RDD: We processed RDD data using modified ChIA-PIPE pipeline. It includes the following main procedures: linker filtering, data alignment and qualification, coverage generation, interaction clustering, quality control, and finally data classification for visualization and further analyzation. Briefly, a configuration file and two FASTQ files (R1 reads and R2 reads) were taken. Firstly, read pairs are scanned for the RDD-linker sequence and partitioned into categories: read pairs with (i) no linker, (ii) one linker and one usable genomic tag, or (iii) a linker and PETs. PETs are aligned to a dm3 reference genome. The analysis-ready BAM file contains uniquely mapped, nonredundant PETs. Secondly, 2D chromatin interaction maps are generated using standardized file formats. Thirdly, using interligation PETs (span ≥ 3 kb), loops are called and then annotated with peak support. Then, the binding peaks of the RNA of interest are identified using SPP or MACS2. The 2D chromatin interaction maps can be viewed in Juicebox.js. The loop file, peak file, coverage file, and domain file can be viewed in BASIC Browser.
ChIA-PET:Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing. After trimming the linkers, the sequences flanking the linker were mapped to the dm3 using bwa-mem and only uniquely aligned (MAPQ ≥ 30) PETs were retained. PCR duplicates were removed using Picard. Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
RNA-seq:the RNA-seq data was processed using STAR and RSEM. Firstly, the raw FASTQ files with pair-end reads were mapped to dm3 genome using STAR with ENCODE standard options. Secondly, FPKM of genes were calculated by utilizing ‘rsem-calculate-expression’ script of RSEM, with key configurations of ‘--paired-end’ and ‘--forward-prob 0’ for selecting reads that derived from the reverse strand. Then the uniquely mapped reads of total RNA-seq were hit and plotted the RPKM as boxplots.
Assembly: dm3
Supplementary files format and content: cluster, hic, bedgraph, peak

growth_protocol: Drosophila S2 cells were cultured in Gibco™ Schneider’s Drosophila Medium supplemented with 10% fetal bovine serum  and maintained at 27 °C.

extract_protocol:
Dual-crosslinked cells were subjected for cell lysis and nuclei lysis. The lysed nuclei are fragmented into smaller complexes by sonication. Then the ncRNA of interest and its associated complexes are purified by hybridization using biotinylated antisense probes of a target ncRNA. And the purified complexes are immobilized on streptavidin C1 beads via high affinity with biotin, the excess unbound sites of beads are specifically blocked with denatured biotins to avoid the adsorption of biotinylated bridge-linker by streptavidin beads in later procedure of proximity ligation. Chromatin DNA contacts of complexes on beads are captured by incorporated biotinylated linkers between DNA sites during proximity ligation. Finally the ligated products are subjected for Tn5 tagmentation and enriched by streptavidin M280 beads for sequencing to obtain the specific RNA associated chromatin DNA–DNA interactions.
The ligated DNA was fragmented by using Tn5 transposase. Then the fragmented DNA contained RDD-linker were captured with Streptavidin beads and used for PCR amplification. These PCR products were then performed double size-selection with AMPure beads to achieve the DNA fragments with size of 300-600 bp, then subjected for Illumina NovaSeq 6000 with paired-end sequencing at read lengths of 150 bp.

treatment_protocol: For heat treatment, the exponential growth phase of cells were aliquot to three tubes, one tube was carried out crosslinking directly (Control, Ctrl), two tubes were subjected to 37 °C for 20 min and then one of them was stepped into crosslinking procedure immediately (heat shock, HS), the other was kept at room temperature for 20 min then was performed crosslinking (Recovery, RC).

value: Control

value: late stage 20-24 hours old Drosophila melanogaster embryos

tag: enriched factor


title: RNA-seq HS

value: Heat shock


title: Donor3_Stimulated_ATM-inhibitor_Day6

description:
150-bp paired end seq
104295-001-015R


title: PANC-1 cells, 0.1% DMSO treated, bioreplicate 1: Ribo-seq

description:
ribosome-protected fragments (RPFs)
PANC-DMSO-1

value: 0.1percent DMSO,24 h


title: Donor3_Stimulated_DNA-PKinhibitor_Day6

description:
150-bp paired end seq
104295-001-014


title: PANC-1 cells, 0.1% DMSO treated, bioreplicate 2: Ribo-seq

description:
ribosome-protected fragments (RPFs)
PANC-DMSO-2


title: CFPAC-1 cells, IKE treated, bioreplicate 2: Ribo-seq

description:
ribosome-protected fragments (RPFs)
CFPAC-IKE-2

value: 10 microM IKE,24 h


title: RNAPII ChIA-PET RC

data_processing:
RDD: We processed RDD data using modified ChIA-PIPE pipeline. It includes the following main procedures: linker filtering, data alignment and qualification, coverage generation, interaction clustering, quality control, and finally data classification for visualization and further analyzation. Briefly, a configuration file and two FASTQ files (R1 reads and R2 reads) were taken. Firstly, read pairs are scanned for the RDD-linker sequence and partitioned into categories: read pairs with (i) no linker, (ii) one linker and one usable genomic tag, or (iii) a linker and PETs. PETs are aligned to a dm3 reference genome. The analysis-ready BAM file contains uniquely mapped, nonredundant PETs. Secondly, 2D chromatin interaction maps are generated using standardized file formats. Thirdly, using interligation PETs (span ≥ 3 kb), loops are called and then annotated with peak support. Then, the binding peaks of the RNA of interest are identified using SPP or MACS2. The 2D chromatin interaction maps can be viewed in Juicebox.js. The loop file, peak file, coverage file, and domain file can be viewed in BASIC Browser.
ChIA-PET:Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing. After trimming the linkers, the sequences flanking the linker were mapped to the dm3 using bwa-mem and only uniquely aligned (MAPQ ≥ 30) PETs were retained. PCR duplicates were removed using Picard. Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
RNA-seq:the RNA-seq data was processed using STAR and RSEM. Firstly, the raw FASTQ files with pair-end reads were mapped to dm3 genome using STAR with ENCODE standard options. Secondly, FPKM of genes were calculated by utilizing ‘rsem-calculate-expression’ script of RSEM, with key configurations of ‘--paired-end’ and ‘--forward-prob 0’ for selecting reads that derived from the reverse strand. Then the uniquely mapped reads of total RNA-seq were hit and plotted the RPKM as boxplots.
Assembly: dm3
Supplementary files format and content: cluster, hic, bedgraph, peak
Library strategy: ChIA-PET

value: Recovery

value: RNAPII


title: RNAPII ChIA-PET HS


title: Donor3_Stimulated_DMSO_vehicle_Day6

description:
150-bp paired end seq
104295-001-013

value: DMSO


title: Stage_IV_Steady_State_3

value: Bone Marrow

value: Bone marrow eosinophil developmental stages

value: wild type

value: steady state


title: Stage_III_IL33_Induced_Eosinophilia_2

value: IL-33 induced eosinophilia


title: CFPAC-1 cells, IKE treated, bioreplicate 1: Ribo-seq

description:
ribosome-protected fragments (RPFs)
CFPAC-IKE-1


title: Stage_III_Steady_State_3


title: RNAPII ChIA-PET Ctrl


title: Donor1_Stimulated_DNA-PKinhibitor_Day6

description:
150-bp paired end seq
104295-001-011

value: Cultured cells

value: Stimulated Naive B-cells

value: Healthy Control


title: Stage_II_Steady_State_3


title: CFPAC-1 cells, 0.1% DMSO treated, bioreplicate 2: Ribo-seq

description:
ribosome-protected fragments (RPFs)
CFPAC-DMSO-2

value: pancreatic adenocarcinoma cells


title: RDD 7SK Rep2 deep sequencing

data_processing:
RDD: We processed RDD data using modified ChIA-PIPE pipeline. It includes the following main procedures: linker filtering, data alignment and qualification, coverage generation, interaction clustering, quality control, and finally data classification for visualization and further analyzation. Briefly, a configuration file and two FASTQ files (R1 reads and R2 reads) were taken. Firstly, read pairs are scanned for the RDD-linker sequence and partitioned into categories: read pairs with (i) no linker, (ii) one linker and one usable genomic tag, or (iii) a linker and PETs. PETs are aligned to a dm3 reference genome. The analysis-ready BAM file contains uniquely mapped, nonredundant PETs. Secondly, 2D chromatin interaction maps are generated using standardized file formats. Thirdly, using interligation PETs (span ≥ 3 kb), loops are called and then annotated with peak support. Then, the binding peaks of the RNA of interest are identified using SPP or MACS2. The 2D chromatin interaction maps can be viewed in Juicebox.js. The loop file, peak file, coverage file, and domain file can be viewed in BASIC Browser.
ChIA-PET:Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing. After trimming the linkers, the sequences flanking the linker were mapped to the dm3 using bwa-mem and only uniquely aligned (MAPQ ≥ 30) PETs were retained. PCR duplicates were removed using Picard. Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
RNA-seq:the RNA-seq data was processed using STAR and RSEM. Firstly, the raw FASTQ files with pair-end reads were mapped to dm3 genome using STAR with ENCODE standard options. Secondly, FPKM of genes were calculated by utilizing ‘rsem-calculate-expression’ script of RSEM, with key configurations of ‘--paired-end’ and ‘--forward-prob 0’ for selecting reads that derived from the reverse strand. Then the uniquely mapped reads of total RNA-seq were hit and plotted the RPKM as boxplots.
Assembly: dm3
Supplementary files format and content: cluster, hic, bedgraph, peak
Library strategy: RDD

value: Wild type


title: RNA-seq RC

value: late stage 20-24 hours old Drosophila melanogaster embryos


title: CFPAC-1 cells, 0.1% DMSO treated, bioreplicate 1: Ribo-seq

description:
ribosome-protected fragments (RPFs)
CFPAC-DMSO-1


title: Stage_I_Steady_State_3


title: Donor1_Stimulated_DMSO_vehicle_Day6

description:
150-bp paired end seq
104295-001-010


title: RDD 7SK Rep2


title: Stage_IV_Steady_State_2


title: Stage_I_IL33_Induced_Eosinophilia_1